We continued improving techniques for topographic mapping of motor cortex using transcranial magnetic stimulation (TMS). We found that motor maps enlarge with acquisition of skills and motor learning, unveiling the role of the primary motor cortex in these cognitive processes. Training to change the timing of execution of two motor acts can enhance their cortical motor representations leading to greater overlapping and suggesting timing is a powerful trigger of cortical plasticity. Patients with cortical strokes (who have recovered) have larger maps of motor output targeting the affected side of the body and lower thresholds for excitation. Cortical motor excitability is increased in dystonia and maps of motor outputs are deranged in the hemisphere contralateral to the dystonic side, a mechanism that could explain the overflow of motor activity in these patients. Magnetic but not electrical stimulation reset postural tremor in Parkinson's disease and essential tremor suggesting an important role of intracortical structures in their generation. Post~exercise facilitation (PEF) of MEPs is decreased while postexercise depression (PED) is not affected in patients with chronic fatigue syndrome and depression. Repetitive transcranial magnetic stimulation (rTMS) delivered over the supplementary motor area (SMA) induces disruption of complex motor sequences with a longer latency than rTMS delivered over primary motor cortex, suggesting an important role for midline structures in advanced planning and performance of complex motor acts. Our studies also suggest a role of the SMA in modulation of segmental reflexes (H-reflexes). We found that the hand may have two ipsilateral cortical representations, one of which, upon stimulation, produces silent periods and the other motor evoked potentials at the same stimulus intensity. Verbal recall was consistently diminished after left midtemporal and bilateral dorsofrontal rTMS. rTMS delivered to the right lateral prefrontal area produces mood elevation and increases in TRH secretion in normal subjects and clinical improvement in patients with refractory depression.